Onychophora in invertebrate conservation: priorities, practice and prospects

The rationale of promoting onychophorans as target taxa in invertebrate conservation is discussed. Current knowledge relevant to onychophoran conservation is outlined and gaps are identified. The prospects for conserving onychophorans are discussed, and priorities suggested.     

How maltose influences structural changes to bind to maltose‐binding protein: Results from umbrella sampling simulation

A well‐studied periplasmic‐binding protein involved in the abstraction of maltose is maltose‐binding protein (MBP), which undergoes a ligand‐induced conformational transition from an open (ligand‐free) to a closed (ligand‐bound) state. Umbrella sampling simulations have been us to estimate the free energy of binding of maltose to MBP and to trace the potential of mean force of the unbinding event using the center‐of‐mass distance between the protein and ligand as the reaction coordinate. The free energy thus obtained compares nicely with the experimentally measured value justifying our theoretical basis. Measurement of the domain angle (N‐terminal‐domain – hinge – C‐terminal‐domain) along the unbinding pathway established the existence of three different states. Starting from a closed state, the protein shifts to an open conformation during the initial unbinding event of the ligand then resides in a semi‐open conformation and later resides predominantly in an open‐state. These transitions along the ligand unbinding pathway have been captured in greater depth using principal component analysis. It is proposed that in mixed‐model, both conformational selection and an induced‐fit mechanism combine to the ligand recognition process in MBP. Proteins 2013. © 2012 Wiley Periodicals, Inc.     

An analysis of genetic variation in natural populations of Sticherus flabellatus [R. Br. (St John)] using amplified fragment length polymorphism (AFLP) markers

Amplified fragment length polymorphisms (AFLPs) were used to characterize the genetic diversity within and among natural populations of Sticherus flabellatus. Eight populations within the Sydney region of New South Wales, Australia were surveyed using 11 primer combinations. A total of 1108 reproducible bands were detected of which 469 (42%) were polymorphic. FST estimates averaged over all polymorphic loci indicated that significant genomic differentiation occurs among populations (average = 0.783). Genetic diversity within populations was assessed according to average heterozygosity (H) and percentage polymorphic loci (P) per population. Within-population diversity ranged from H = 0.12 and P = 33.69 to H = 0.04 and P = 15.99. Analysis of genetic similarity among populations suggested that the eight populations studied fall into two groups of four populations, based on population size and the condition of the habitat. Phenetic analysis (AMOVA) indicated that genetic variation is greater among populations (74.34%) than within populations (25.66%). These findings suggest that the breeding system of S. flabellatus is predominantly inbreeding, with genetic diversity maintained by occasional outcrossing in larger populations. The results presented in this study could provide evidence to support the proposal to protect natural stands of S. flabellatus, which has implications for the Australian horticulture industry.     

Molecular dynamics simulations investigate the pathway of substrate entry active site of rhomboid protease

Rhomboid proteases can catalyze peptide bond cleavage and participate in abundant biological processes encompassing all branches of life; however, the pathway for substrate entry into its active site remains ambiguous. Here, the two possible pathways are preliminarily determined through molecular dynamics: One pathway is between Tm2 and Tm5, and the other is between Loop3 and Loop5. Then, the umbrella sampling simulations are performed to investigate the more feasible pathway for substrate entry. The results show that free energy barriers along the two pathways are similar; in the pathway 1, Trp236 and Trp157 as pivotal residues are responsible for the rotation of substrate in the binding process; in the pathway 2, among some important residues, the residue His150 plays an important role in substrate entry. Further, combining with previous experiment results, it is concluded that the substrate is inclined to enter into the active site along pathway 2. Our results are important for further understanding the function and catalysis mechanism of rhomboid proteases.

Communicated by Ramaswamy H. Sarma     

Indications of higher diversity and abundance of small rodents in human‐influenced Sudanian savannah than in the Niokolo Koba National Park (Senegal)

Expansion of human activities in the Sudanian savannah is changing natural habitats together with their animal communities. The abundance and diversity of small mammal communities were investigated in human‐influenced savannahs in close proximity to Niokolo Koba National Park (NKNP) in south‐eastern Senegal and compared with those from NKNP. Two localities were sampled in natural and two in human‐influenced areas during two dry and two rainy seasons. Total sampling effort was 5400 trap‐nights. Ninety‐eight individuals of eleven species were captured outside NKNP, while only 28 individuals of five rodent species were caught inside the park (all of which were found also outside NKNP). The most abundant species outside NKNP was Mastomys erythroleucus, while inside NKNP it was Praomys daltoni. Both relative abundance and diversity were significantly higher in human‐influenced landscape than in natural savannahs of NKNP. The difference in species richness may be linked with lower population densities of certain species in NKNP and the effect of traditional agriculture, which may support the presence of species typical for deforested landscape. Furthermore, food availability, and predator abundances are discussed as possible reasons for the higher rodent abundances outside NKNP.     

Ramachandran free-energy surfaces for disaccharides: trehalose, a case study

We present calculated potential of mean force surfaces for rotation about phi, psi dihedral angles of the alpha(1<-->1)alpha-glycosidic linkage in the disaccharide trehalose (alpha-D-Glc-(1<-->1)-alpha-D-Glc) in both vacuum and aqueous solution. The effects of aqueous solvation upon the alpha(1<-->1)alpha-glycosidic linkage are investigated through comparison of the vacuum and aqueous solution free-energy surfaces. These surfaces reveal that trehalose is restricted to a single minimum-energy conformation in both vacuum and solution. The exceptional rigidity of this disaccharide in solution may provide a molecular rationale for the antidesiccant properties of trehalose glasses.     

Sciadopitys cladodes from Eocene Baltic amber

The Baltic amber deposit represents the largest accumulation of any fossil resin worldwide and hundreds of thousands of entrapped arthropods have been recovered so far. The source plants of Baltic amber, however, are still controversial, and the botanical composition of the ‘Baltic amber forest’ remains poorly studied. Here, we provide the first unequivocal Baltic amber inclusions of the umbrella pine Sciadopitys (Sciadopityaceae), a genus that has been suggested as the source of succinite (the main variety of Baltic amber) based on chemical analyses. As previously suggested sciadopitoid inclusions must be reconsidered as being notional, representing angiosperm leaves instead, the new fossils are the first unambiguous macrofossil evidence of Sciadopitys from the ‘Baltic amber forest’, and the first pre‐Oligocene macrofossil record of Sciadopitys from Europe. The fossil Sciadopitys cladodes provide new insights into the conifer diversity of the ‘Baltic amber forest’ and broaden the picture of its palaeoecology, indicating the presence of humid swamp to raised bog habitats. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2016, 180 , 258–268.     

Sparse sampling of water density fluctuations near liquid-vapor coexistence

Abstract

The free energetics of water density fluctuations in bulk water, at interfaces, and in hydrophobic confinement inform the hydration of hydrophobic solutes as well as their interactions and assembly. The characterisation of such free energetics is typically performed using enhanced sampling techniques such as umbrella sampling. In umbrella sampling, order parameter distributions obtained from adjacent biased simulations must overlap in order to estimate free energy differences between biased ensembles. Many biased simulations are typically required to ensure such overlap, which exacts a steep computational cost. We recently introduced a sparse sampling method, which circumvents the overlap requirement by using thermodynamic integration to estimate free energy differences between biased ensembles. Here we build upon and generalise sparse sampling for characterising the free energetics of water density fluctuations in systems near liquid-vapor coexistence. We also introduce sensible heuristics for choosing the biasing potential parameters and strategies for adaptively refining them, which facilitate the estimation of such free energetics accurately and efficiently. We illustrate the method by characterising the free energetics of cavitation in a large volume in bulk water. We also use sparse sampling to characterise the free energetics of capillary evaporation for water confined between two hydrophobic plates. In both cases, sparse sampling is nearly two orders of magnitude faster than umbrella sampling. Given its efficiency, the sparse sampling method is particularly well suited for characterising free energy landscapes for systems wherein umbrella sampling is prohibitively expensive.     

Behavior of the ATP grasp domain of biotin carboxylase monomers and dimers studied using molecular dynamics simulations

The enzyme biotin carboxylase (BC) uses adenosine triphosphate (ATP) to carboxylate biotin and is involved in fatty acid synthesis. Structural evidence suggests that the B domain of BC undergoes a large hinge motion of ～45° when binding and releasing substrates. Escherichia coli BC can function as a natural homodimer and as a mutant monomer. Using molecular dynamics simulations, we evaluate the free energy profile along a closure angle of the B domain of E. coli BC for three cases: a monomer without bound Mg(2)ATP, a monomer with bound Mg(2)ATP, and a homodimer with bound Mg(2)ATP in one subunit. The simulation results show that a closed state is the most probable for the monomer with or without bound Mg(2)ATP. For the dimer with Mg(2)ATP in one of its subunits, communication between the two subunits was observed. Specifically, in the dimer, the opening of the subunit without Mg(2)ATP caused the other subunit to open, and hysteresis was observed upon reclosing it. The most stable state of the dimer is one in which the B domain of both subunits is closed; however, the open state for the B domain without Mg(2)ATP is only approximately 2k(B)T higher in free energy than the closed state. A simple diffusion model indicates that the mean times for opening and closing of the B domain in the monomer with and without Mg(2)ATP are much smaller than the overall reaction time, which is on the order of seconds.     

Priority sites for conservation of land snails in Gabon: testing the umbrella species concept

In order to assess the potential for molluscan conservation of a protected area considered representative of regional megafauna, we sampled molluscs inside and outside Lopé National Park in Gabon. In the northern part of Lopé National Park, 116 stations were surveyed and 71 species collected. Outside the park, 37 stations yielded 96 species, including 71 in Lastoursville, a small limestone area where molluscs are significantly more abundant than in other collecting sites. Lastoursville is among the richest sites known for molluscs in Africa. Overlap between sampling areas was limited, with 20.0% of the species found only in Lopé National Park, and 40.8% of the species found only outside. This suggests that Lopé National Park does not protect the whole molluscan diversity of central Gabon. Given the high levels of allopatric diversity of tropical land snails, conservation strategies cannot be the same for snails and for wide-ranging vertebrates. Protecting small areas with a high abundance and diversity of molluscs would be less expensive and as efficient for molluscan conservation as protecting large tracts of rainforest. Despite limited general knowledge of central African molluscs, robust estimates of site-specific diversity can be produced. Limestone areas harbour a remarkable biodiversity: sites such as Lastoursville would be ideal candidates for small protected areas dedicated to the conservation of land snails, and would complement the role of large protected areas.     

Does one size fit all? A multispecies approach to regional landscape corridor planning

Aim

The practical value of the single‐species approach to conserve biodiversity could be minimal or negligible when sympatric species are limited by factors that are not relevant to the proposed umbrella species. In this study, we quantitatively evaluated as follows: (1) habitat suitability and potential movement corridors of a single umbrella species, giant panda (Ailuropoda melanoleuca); (2) habitat suitability of sympatric mammals; and (3) the potential effectiveness of the single‐species corridor planning to preserve suitable habitat and its connectivity of other focal species.

Location

Qinling Mountains, central part of China (15,000 km²).

Methods

We collected species distribution, environmental and anthropogenic data and conducted species occupancy modelling for giant panda and six other sympatric species (i.e., takin Budorcas taxicolor, tufted deer Elaphodus cephalophus, Chinese goral Naemorhedus griseus, Reeve's muntjac Muntiacus reevesi, leopard cat Prionailurus bengalensis and yellow‐throated marten Martes flavigula). We then conducted circuit models to identify potential corridors for each species and evaluated the effectiveness of giant panda corridors to restore the habitat connectivity for these sympatric mammals.

Results

Occupancy modelling revealed that each species had a unique set of environmental variables associated with its distribution in the Qinling Mountains. We found that giant panda and all other focal species had some degree of fragmentation to their suitable habitat that required restoring habitat connectivity. Among the eight potential giant panda corridors, conservation efforts to reduce anthropogenic impacts would significantly improve the effectiveness of six corridors, while the other two corridors would require altering the vegetation. Five proposed giant panda corridors had remarkable overlap with corridors proposed for other species. We suggest two giant panda corridors as a priority due to their potential to maximize the benefits to both giant panda and a broader suite of mammals.

Main conclusions

Corridor planning in this region of China will likely continue using the single‐species policy, but our results highlight that not all potential giant panda corridors have equal effectiveness for other wildlife species. When offered multiple alternative actions, conservation planners can prioritize corridor development based on a multispecies perspective without loss of connectivity for the priority species. This approach has strong implications to the conservation of wildlife communities in China, and elsewhere, where conservation plans developed for a single‐species garner most available funding and institutional support.

     

Dimensionality reduction of free energy profiles of benzene in silicalite-1: calculation of diffusion coefficients using transition state theory

This study describes the development and application of a new computational methodology for calculating the self-diffusivity of sorbate molecules strongly confined within shape-selective nanoporous materials. An umbrella sampling strategy, employing repulsive walls to confine the sorbate within specific regions of the pore space, is invoked to extract free energy profiles with respect to the sorbate degrees of freedom. Based on these profiles, it is shown how the multidimensional problem of translational diffusion of benzene in flexible silicalite-1 can be reduced first to a six-dimensional problem, then to a three-dimensional (3D) problem and finally, to a 1D problem. A 3D free energy distribution is accumulated as a function of the benzene centre of mass position and ultimately reduced to a set of 1D profiles for the benzene centre of mass along the pore axes. From these profiles, the rate constants for jumps executed by benzene between sorption sites are calculated using transition state theory; from the latter rate constants, the low-occupancy self-diffusivity is obtained using the MESoRReD method [Kolokathis PD, Theodorou DN. On solving the master equation in spatially periodic systems. J Chem Phys. 2012;137:034112]. The activation energy for diffusion and preferred orientations in the various sorption states in silicalite are in very favourable agreement with available experimental measurements.     

Reptiles Under the Conservation Umbrella of the Greater Sage-Grouse

In conservation paradigms, management actions for umbrella species also benefit co-occurring species because of overlapping ranges and similar habitat associations. The greater sage-grouse (Centrocercus urophasianus) is an umbrella species because it occurs across vast sagebrush ecosystems of western North America and is the recipient of extensive habitat conservation and restoration efforts that might benefit sympatric species. Biologists' understanding of how non-target species might benefit from sage-grouse conservation is, however, limited. Reptiles, in particular, are of interest in this regard because of their relatively high diversity in shrublands and grasslands where sage-grouse are found. Using spatial overlap of species distributions, land cover similarity statistics, and a literature review, we quantified which reptile species may benefit from the protection of intact sage-grouse habitat and which may be affected by recent (since about 1990) habitat restoration actions targeting sage-grouse. Of 190 reptile species in the United States and Canadian provinces where greater sage-grouse occur, 70 (37%) occur within the range of the bird. Of these 70 species, about a third (11 snake and 11 lizard species) have >10% of their distribution area within the sage-grouse range. Land cover similarity indices revealed that 14 of the 22 species (8 snake and 6 lizard species) had relatively similar land cover associations to those of sage-grouse, suggesting greater potential to be protected under the sage-grouse conservation umbrella and greater potential to be affected, either positively or negatively, by habitat management actions intended for sage-grouse. Conversely, the remaining 8 species are less likely to be protected because of less overlap with sage-grouse habitat and thus uncertain effects of sage-grouse habitat management actions. Our analyses of treatment databases indicated that from 1990 to 2014 there were at least 6,400 treatments implemented on public land that covered approximately 4 million ha within the range of the sage-grouse and, of that, >1.5 million ha were intended to at least partially benefit sage-grouse. Whereas our results suggest that conservation of intact sagebrush vegetation communities could benefit ≥14 reptiles, a greater number than previously estimated, additional research on each species' response to habitat restoration actions is needed to assess broader claims of multi-taxa benefits when it comes to manipulative sage-grouse habitat management. Published 2020. This article is a U.S. Government work and is in the public domain in the USA.     

Investigations of Takeout proteins’ ligand binding and release mechanism using molecular dynamics simulation

Takeout (To) proteins exist in a diverse range of insect species. They are involved in many important processes of insect physiology and behaviors. As the ligand carriers, To proteins can transport the small molecule to the target tissues. However, ligand release mechanism of To proteins is unclear so far. In this contribution, the process and pathway of the ligand binding and release are revealed by conventional molecular dynamics simulation, steered molecular dynamics simulation and umbrella sampling methods. Our results show that the α4-side of the protein is the unique gate for the ligand binding and release. The structural analysis confirms that the internal cavity of the protein has high rigidity, which is in accordance with the recent experimental results. By using the potential of mean force calculations in combination with residue cross correlation calculation, we concluded that the binding between the ligand and To proteins is a process of conformational selection. Furthermore, the conformational changes of To proteins and the hydrophobic interactions both are the key factors for ligand binding and release.     

Kinetics and thermodynamics of gas diffusion in a NiFe hydrogenase

We have investigated O₂ and H₂ transport across a NiFe hydrogenase at the atomic scale by means of computational methods. The Wild Type protein has been compared with the V74Q mutant. Two distinct methodologies have been applied to study the gas access to the active site. Temperature locally enhanced sampling simulations have emphasized the importance of protein dynamics on gas diffusion. The O₂ diffusion free energy profiles, obtained by umbrella sampling, are in agreement with the known kinetic data and show that in the V74Q mutant, the inhibition process is lowered from both a kinetic and a thermodynamic point of view. Proteins 2011. © 2012 Wiley Periodicals, Inc.     

Flexibility and charge asymmetry in the activation loop of Src tyrosine kinases

Regulated activity of Src kinases is critical for cell growth. Src kinases can be activated by trans-phosphorylation of a tyrosine located in the central activation loop of the catalytic domain. However, because the required exposure of this tyrosine is not observed in the down-regulated X-ray structures of Src kinases, transient partial opening of the activation loop appears to be necessary for such processes. Umbrella sampling molecular dynamics simulations are used to characterize the free energy landscape of opening of the hydrophilic part of the activation loop in the Src kinase Hck. The loop prefers a partially open conformation where Tyr416 has increased accessibility, but remains partly shielded. An asymmetric distribution of the charged residues in the sequence near Tyr416, which contributes to shielding, is found to be conserved in Src family members. A conformational equilibrium involving exchange of electrostatic interactions between the conserved residues Glu310 and Arg385 or Arg409 affects activation loop opening. A mechanism for access of unphosphorylated Tyr416 into an external catalytic site is suggested based on these observations.     

Attributes of trees used by nesting and foraging woodpeckers (Aves: Picidae) in an area with old pollarded Oaks (Quercus spp.) in the Taurus Mountains,Turkey

We used three woodpecker species as umbrella species for old deciduous forests, and analysed their preferences in an area with old pollarded oaks in the Taurus Mountains, Turkey. Using plot inventories, we physically characterised trees utilised for nesting and foraging amongst woodpeckers in general and the Middle Spotted Woodpecker (Leiopicus medius) in particular. Trees more frequently visited by foraging woodpeckers differed from randomly chosen trees by being taller, having a larger circumference, greater bark furrow depth and shorter distance to neighbouring trees. Nesting trees were taller, had a higher proportion of dead wood but a lower surface area of natural cavities. Our results suggest that the woodpeckers in the study area rely upon woodlands containing mature trees, thus have the potential to function as suitable umbrella species’ to highlight the conservation value of oak forest habitats in southern Turkey.     

指示种、伞护种与旗舰种:有关概念及其在保护生物学中的应用

指示种、伞护种和旗舰种等的运用常常可以作为解决保护生物学问题的捷径。指示种被用来评价环境中人为干扰因素的程度,监测其他物种的种群动态,或用于确定生物多样性较高的区域;伞护种则常用来确定需保护生境的类型和面积;而旗舰种被用于引起公众对保护行为的关注。本文试图对上述术语和概念在使用上加以明确区分,并对其应用提出一些指导性原则。认为针对上述不同类型的代理种,使用的目的和选择的标准应有所不同,彼此不能混淆使用。     

Freshwater megafauna diversity: Patterns,status and threats

Aim

Freshwater megafauna remain underrepresented in research and conservation, despite a disproportionately high risk of extinction due to multiple human threats. Therefore, our aims are threefold; (i) identify global patterns of freshwater megafauna richness and endemism, (ii) assess the conservation status of freshwater megafauna and (iii) demonstrate spatial and temporal patterns of human pressure throughout their distribution ranges.

Location

Global.

Methods

We identified 207 extant freshwater megafauna species, based on a 30 kg weight threshold, and mapped their distributions using HydroBASINS subcatchments (level 8). Information on conservation status and population trends for each species was extracted from the IUCN Red List website. We investigated human impacts on freshwater megafauna in space and time by examining spatial congruence between their distributions and human pressures, described by the Incident Biodiversity Threat Index and Temporal Human Pressure Index.

Results

Freshwater megafauna occur in 76% of the world’s main river basins (level 3 HydroBASINS), with species richness peaking in the Amazon, Congo, Orinoco, Mekong and Ganges‐Brahmaputra basins. Freshwater megafauna are more threatened than their smaller counterparts within the specific taxonomic groups (i.e., fishes, mammals, reptiles and amphibians). Out of the 93 freshwater megafauna species with known population trends, 71% are in decline. Meanwhile, IUCN Red List assessments reported insufficient or outdated data for 43% of all freshwater megafauna species. Since the early 1990s, human pressure has increased throughout 63% of their distribution ranges, with particularly intense impacts occurring in the Mekong and Ganges‐Brahmaputra basins.

Main conclusions

Freshwater megafauna species are threatened globally, with intense and increasing human pressures occurring in many of their biodiversity hotspots. We call for research and conservation actions for freshwater megafauna, as they are highly sensitive to present and future pressures including a massive boom in hydropower dam construction in their biodiversity hotspots.